Bottom Line:
More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade.Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation.Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.

Background: Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis.

Results: More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs.

Conclusions: Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.

Mentions:
Phylogenetic tree based on the partial sequence of 18 s rRNA, ITS1, 5.8 s rRNA complete sequence, ITS2 and 28 s rRNA partial sequence revealed that Ci 6684 belongs to Candida auris clade of Korean and Indian isolates with 99 % bootstrapped confidence (Fig. 2a). To further confirm its origin, we performed multiple sequence alignment with the Indian C. auris isolates and found complete conservation of rRNA and ITS sequences (Additional file 5). The same isolate was also able to grow at 40 °C and 42 °C as reported for C. auris but not for C. haemulonii [20]. Electrophoretic karyotyping by PFGE of Ci6684 yielded 5 bands and the pattern was similar to that reported previously for C. auris [26] (Fig. 2b). Because diagnostic laboratories rely only on automated systems like Vitek 2 or APIC20C which routinely identifies C. auris as C. haemulonii or C. famata, the actual occurrence of C. auris fungemia is under reported [25, 27, 28]. Our results emphasize the need to develop accurate species identification system based on molecular typing methods to ensure proper management of fungemia. Another recently developed method for identifying C. auris by MALDI-TOF has also been reported [29]. Henceforth Ci 6684 will be referred to C. auris 6684 in the remaining study.Fig. 2

Mentions:
Phylogenetic tree based on the partial sequence of 18 s rRNA, ITS1, 5.8 s rRNA complete sequence, ITS2 and 28 s rRNA partial sequence revealed that Ci 6684 belongs to Candida auris clade of Korean and Indian isolates with 99 % bootstrapped confidence (Fig. 2a). To further confirm its origin, we performed multiple sequence alignment with the Indian C. auris isolates and found complete conservation of rRNA and ITS sequences (Additional file 5). The same isolate was also able to grow at 40 °C and 42 °C as reported for C. auris but not for C. haemulonii [20]. Electrophoretic karyotyping by PFGE of Ci6684 yielded 5 bands and the pattern was similar to that reported previously for C. auris [26] (Fig. 2b). Because diagnostic laboratories rely only on automated systems like Vitek 2 or APIC20C which routinely identifies C. auris as C. haemulonii or C. famata, the actual occurrence of C. auris fungemia is under reported [25, 27, 28]. Our results emphasize the need to develop accurate species identification system based on molecular typing methods to ensure proper management of fungemia. Another recently developed method for identifying C. auris by MALDI-TOF has also been reported [29]. Henceforth Ci 6684 will be referred to C. auris 6684 in the remaining study.Fig. 2

Bottom Line:
More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade.Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation.Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.

Background: Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis.

Results: More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs.

Conclusions: Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.